Classifying acoustic units is often a key step in studying repertoires and sequence structure in animal communication. Manual classification by eye and ear remains the primary method, but new tools and techniques are urgently needed to expedite the process for large, diverse datasets. Here we introduce Koe, an application for classifying and analysing animal vocalizations. Koe offers bulk‐labelling of units via interactive ordination plots and unit tables, as well as visualization and playback, segmentation, measurement, data filtering/exporting and new tools for analysing repertoire and sequence structure – in an integrated environment. We demonstrate Koe with a real‐world case study of New Zealand bellbird Anthornis melanura songs from an archipelago metapopulation. Having classified 21,500 units in Koe, we compare repertoires and sequence structure between sites and sexes. Koe is web‐based (koe.io.ac.nz.) and easy to use, making it ideal for collaboration, education and citizen science. By enabling large‐scale, high‐resolution classification and analysis of animal vocalizations, Koe expands the possibilities for bioacoustics research.

Despite the known benefit of considering welfare within wildlife conservation and management, there remains a lack of data to inform such evaluations. To assess animal welfare, relevant information must be captured scientifically and systematically. A key first step is identifying potential indicators of welfare and the practicality of their measurement. We assessed the feasibility of evaluating potential welfare indicators from opportunistically gathered video footage of four stranded odontocete species (n = 53) at 14 stranding events around New Zealand. The first stranded cetacean ethogram was compiled, including 30 different behaviours, 20 of which were observed in all four species. Additionally, thirteen types of human intervention were classified. A subset of 49 live stranded long-finned pilot whales (Globicephala melas edwardii) were assessed to determine indicator prevalence and to quantify behaviours. Four ‘welfare status’ and six ‘welfare alerting’ non-behavioural indicators could be consistently evaluated from the footage. Additionally, two composite behavioural indicators were feasible. Three human intervention types (present, watering, and touching) and five animal behaviours (tail flutter, dorsal fin flutter, head lift, tail lift, and head side-to-side) were prevalent (>40% of individuals). Our study highlights the potential for non-invasive, remote assessments via video footage and represents an initial step towards developing a systematic, holistic welfare assessment framework for stranded cetaceans.

Dolphin photo-identification has traditionally relied only on distinctive markings on the dorsal fin—this is problematic for delphinids whose populations exhibit a low mark ratio. We used common dolphins (genus Delphinus) as a model species to assess the viability of using pigmentation for photo-identification. Using a photo-identification catalogue of 169 adult individuals collected between 2002 and 2013, we extracted features that quantified pigmentation in a manner that was robust to lighting artefacts and dorsal fin orientation. We determined the proportion of individuals which exhibited pigmentation and examined temporal stability by (i) visually examining individuals and (ii) testing for seriation. We found 88–91% of images could be manually matched to the correct individual in the catalogue based on pigmentation patterns alone. A linear discriminant analysis classifier correctly identified the correct individual 77% of the time. We found 95% common dolphins exhibited distinctive pigmentation—all of which were temporarily stable. Our work challenges the current thinking that pigmentation is an unreliable feature for delphinid photo-identification and suggests that this feature could be applied to common dolphins and other poorly-marked delphinids.

Wildlife management can influence animal welfare and survival, although both are often not explicitly integrated into decision making. This study explores fundamental concepts and key concerns relating to the welfare and survival of stranded cetaceans. Using the Delphi method, the opinions of an international, interdisciplinary expert panel were gathered, regarding the characterisation of stranded cetacean welfare and survival likelihood, knowledge gaps and key concerns. Experts suggest that stranded cetacean welfare should be characterised based on interrelated aspects of animals’ biological function, behaviour, and mental state and the impacts of human interventions. The characterisation of survival likelihood should reflect aspects of stranded animals’ biological functioning and behaviour as well as a 6-month post-re-floating survival marker. Post-release monitoring was the major knowledge gap for survival. Welfare knowledge gaps related to diagnosing internal injuries, interpreting behavioural and physiological parameters, and euthanasia decision making. Twelve concerns were highlighted for both welfare and survival likelihood, including difficulty breathing and organ compression, skin damage and physical traumas, separation from conspecifics, and suffering and stress due to stranding and human intervention. These findings indicate inextricable links between perceptions of welfare state and the likely survival of stranded cetaceans and demonstrate a need to integrate welfare science alongside conservation biology to achieve effective, ethical management at strandings.

Management of live cetacean strandings generally focuses on refloating animals, yet there is a lack of scientific data to inform decision-making. Valid indicators that are practical to measure are needed to assess welfare status and survival likelihood for stranded cetaceans. The Delphi method was applied to gather international and interdisciplinary expert opinion to provide face validity to potential indicators of stranded cetacean welfare and survival likelihood. Two online questionnaires were conducted. In the first questionnaire these experts identified potential indicators of stranded cetacean welfare and survival likelihood. These indicators were subsequently scored by the same experts in questionnaire two, based on their value for assessing welfare/survival likelihood and being practical to measure. Indicators considered valuable and practical for assessing welfare and survival likelihood at strandings included animal-based indices of body and skin condition, signs of physical trauma, respiration rate and various behaviours. Resource-/management-based indicators related mainly to human intervention and should be correlated with animal-based indices to provide relevant evaluations. Importantly, inextricable links between welfare and survival for stranded cetaceans are emphasized, with 90% of indicators being similar for both. Investigations into these indicators should be conducted to develop a practical, science-based assessment framework to inform decision-making during stranding events.

Following general anaesthesia (GA), patients frequently experience sleep disruption and fatigue, which has been hypothesized to result at least in part by GA affecting the circadian clock. Here, we provide the first comprehensive time-dependent analysis of the effects of the commonly administered inhalational anaesthetic, isoflurane, on the murine circadian clock, by analysing its effects on (a) behavioural locomotor rhythms and (b) PER2::LUC expression in the suprachiasmatic nuclei (SCN) of the mouse brain. Behavioural phase shifts elicited by exposure of mice (n = 80) to six hours of GA (2% isoflurane) were determined by recording wheel-running rhythms in constant conditions (DD). Phase shifts in PER2::LUC expression were determined by recording bioluminescence in organotypic SCN slices (n = 38) prior to and following GA exposure (2% isoflurane). Full phase response curves for the effects of GA on behaviour and PER2::LUC rhythms were constructed, which show that the effects of GA are highly time-dependent. Shifts in SCN PER2 expression were much larger than those of behaviour (c. 0.7 h behaviour vs. 7.5 h PER2::LUC). We discuss the implications of this work for understanding how GA affects the clock, and how it may inform the development of chronotherapeutic strategies to reduce GA-induced phase-shifting in patients.